Multiple sequence alignment - TraesCS2D01G175500

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G175500 chr2D 100.000 4183 0 0 1 4183 119064979 119060797 0.000000e+00 7725.0
1 TraesCS2D01G175500 chr2D 84.758 269 41 0 1514 1782 246264950 246265218 1.920000e-68 270.0
2 TraesCS2D01G175500 chr2B 93.509 3374 191 15 816 4183 171027145 171023794 0.000000e+00 4992.0
3 TraesCS2D01G175500 chr2B 86.842 494 38 11 205 685 171027615 171027136 1.030000e-145 527.0
4 TraesCS2D01G175500 chr2B 97.727 44 1 0 1762 1805 305091491 305091534 4.480000e-10 76.8
5 TraesCS2D01G175500 chr2A 94.873 1892 76 11 826 2703 121138902 121137018 0.000000e+00 2937.0
6 TraesCS2D01G175500 chr2A 90.539 761 63 6 2697 3456 121135078 121134326 0.000000e+00 998.0
7 TraesCS2D01G175500 chr2A 85.613 702 60 20 1 685 121139583 121138906 0.000000e+00 699.0
8 TraesCS2D01G175500 chr2A 100.000 44 0 0 1762 1805 319285736 319285693 9.640000e-12 82.4
9 TraesCS2D01G175500 chr7A 80.284 634 97 16 1148 1775 651514617 651515228 1.770000e-123 453.0
10 TraesCS2D01G175500 chr4B 79.196 572 84 20 1148 1715 419519948 419520488 8.550000e-97 364.0
11 TraesCS2D01G175500 chr4D 87.625 299 29 4 1484 1782 365013132 365012842 1.440000e-89 340.0
12 TraesCS2D01G175500 chr1B 82.906 351 54 6 1429 1774 335667711 335667362 1.130000e-80 311.0
13 TraesCS2D01G175500 chr7B 81.972 355 57 6 1427 1774 95463299 95463653 1.140000e-75 294.0
14 TraesCS2D01G175500 chr1D 76.766 637 81 27 1148 1782 297773925 297773354 1.140000e-75 294.0
15 TraesCS2D01G175500 chr6A 85.253 217 32 0 1566 1782 405284444 405284660 1.510000e-54 224.0
16 TraesCS2D01G175500 chr5D 88.889 117 4 1 1689 1805 331343818 331343925 7.290000e-28 135.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G175500 chr2D 119060797 119064979 4182 True 7725.000000 7725 100.000000 1 4183 1 chr2D.!!$R1 4182
1 TraesCS2D01G175500 chr2B 171023794 171027615 3821 True 2759.500000 4992 90.175500 205 4183 2 chr2B.!!$R1 3978
2 TraesCS2D01G175500 chr2A 121134326 121139583 5257 True 1544.666667 2937 90.341667 1 3456 3 chr2A.!!$R2 3455
3 TraesCS2D01G175500 chr7A 651514617 651515228 611 False 453.000000 453 80.284000 1148 1775 1 chr7A.!!$F1 627
4 TraesCS2D01G175500 chr4B 419519948 419520488 540 False 364.000000 364 79.196000 1148 1715 1 chr4B.!!$F1 567
5 TraesCS2D01G175500 chr1D 297773354 297773925 571 True 294.000000 294 76.766000 1148 1782 1 chr1D.!!$R1 634

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
285 296 0.366871 CTTGCCGAGTCGTTTGATCG 59.633 55.000 12.31 0.0 36.24 3.69 F
792 819 0.383949 TTTTGGCTTCGTGGACAAGC 59.616 50.000 0.00 0.0 44.79 4.01 F
1630 1680 0.721718 GTGTGATGCTTGCTACGACC 59.278 55.000 0.00 0.0 0.00 4.79 F
2018 2069 1.080093 TCTTGTAGTTGCTCGCCGG 60.080 57.895 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1680 0.460987 GCCTGGAGTGGATCAAGTCG 60.461 60.000 0.0 0.0 0.00 4.18 R
2719 4716 1.127582 GAGCAAACTCAGTGCGATGTC 59.872 52.381 0.0 0.0 46.86 3.06 R
3130 5128 0.036875 AGCTGAGTACAAGGGTTGCC 59.963 55.000 0.0 0.0 0.00 4.52 R
3832 5835 0.039074 ACGAAGAGTGGAAGCAGTCG 60.039 55.000 0.0 0.0 0.00 4.18 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.962253 GTGCCCGCATCGCTACTC 60.962 66.667 0.00 0.00 0.00 2.59
36 37 1.004862 CTCCCTTCAACTTCTTCCCCC 59.995 57.143 0.00 0.00 0.00 5.40
38 39 1.429299 CCCTTCAACTTCTTCCCCCTT 59.571 52.381 0.00 0.00 0.00 3.95
39 40 2.555448 CCCTTCAACTTCTTCCCCCTTC 60.555 54.545 0.00 0.00 0.00 3.46
41 42 0.690762 TCAACTTCTTCCCCCTTCCG 59.309 55.000 0.00 0.00 0.00 4.30
42 43 0.400594 CAACTTCTTCCCCCTTCCGT 59.599 55.000 0.00 0.00 0.00 4.69
43 44 0.691332 AACTTCTTCCCCCTTCCGTC 59.309 55.000 0.00 0.00 0.00 4.79
44 45 1.199425 ACTTCTTCCCCCTTCCGTCC 61.199 60.000 0.00 0.00 0.00 4.79
45 46 1.151987 TTCTTCCCCCTTCCGTCCA 60.152 57.895 0.00 0.00 0.00 4.02
46 47 0.549169 TTCTTCCCCCTTCCGTCCAT 60.549 55.000 0.00 0.00 0.00 3.41
47 48 0.981277 TCTTCCCCCTTCCGTCCATC 60.981 60.000 0.00 0.00 0.00 3.51
48 49 0.983378 CTTCCCCCTTCCGTCCATCT 60.983 60.000 0.00 0.00 0.00 2.90
49 50 0.549169 TTCCCCCTTCCGTCCATCTT 60.549 55.000 0.00 0.00 0.00 2.40
50 51 0.549169 TCCCCCTTCCGTCCATCTTT 60.549 55.000 0.00 0.00 0.00 2.52
73 74 1.574702 GGCGAACGGAAGAAACCCAG 61.575 60.000 0.00 0.00 0.00 4.45
77 78 2.746277 CGGAAGAAACCCAGCCCG 60.746 66.667 0.00 0.00 0.00 6.13
111 112 4.208686 GCTTCCTCCCGCGACGAT 62.209 66.667 8.23 0.00 0.00 3.73
130 140 4.610714 GCCTCCGAATCCTCGCCC 62.611 72.222 0.00 0.00 44.04 6.13
264 275 8.368668 ACGATTGATTTAGCTTAGCTACCTTAT 58.631 33.333 14.08 5.39 41.12 1.73
285 296 0.366871 CTTGCCGAGTCGTTTGATCG 59.633 55.000 12.31 0.00 36.24 3.69
288 300 0.572590 GCCGAGTCGTTTGATCGATG 59.427 55.000 12.31 0.00 41.78 3.84
299 312 6.954058 TCGTTTGATCGATGACGCAGTATTG 61.954 44.000 0.54 0.00 36.24 1.90
381 399 1.300465 CGGCTGATCGACCCATCTG 60.300 63.158 0.00 0.00 0.00 2.90
429 449 1.153353 CCCAATTGCTTGCTTGCTTG 58.847 50.000 0.00 1.24 0.00 4.01
435 455 2.625823 GCTTGCTTGCTTGCCCGTA 61.626 57.895 0.00 0.00 0.00 4.02
449 469 1.736681 GCCCGTAGACGCTAGGTATAG 59.263 57.143 0.00 0.00 38.18 1.31
452 472 3.055819 CCCGTAGACGCTAGGTATAGGTA 60.056 52.174 0.00 0.00 38.18 3.08
453 473 4.383552 CCCGTAGACGCTAGGTATAGGTAT 60.384 50.000 0.00 0.00 38.18 2.73
454 474 5.163405 CCCGTAGACGCTAGGTATAGGTATA 60.163 48.000 0.00 0.00 38.18 1.47
455 475 5.751028 CCGTAGACGCTAGGTATAGGTATAC 59.249 48.000 0.00 0.00 36.97 1.47
459 479 4.256920 ACGCTAGGTATAGGTATACGTGG 58.743 47.826 8.32 9.59 39.48 4.94
461 481 4.593956 GCTAGGTATAGGTATACGTGGGT 58.406 47.826 8.32 0.00 39.48 4.51
462 482 5.626809 CGCTAGGTATAGGTATACGTGGGTA 60.627 48.000 8.32 0.00 39.48 3.69
463 483 6.180472 GCTAGGTATAGGTATACGTGGGTAA 58.820 44.000 8.32 0.00 39.48 2.85
465 485 6.454223 AGGTATAGGTATACGTGGGTAAGA 57.546 41.667 8.32 0.00 39.48 2.10
467 487 5.124617 GGTATAGGTATACGTGGGTAAGAGC 59.875 48.000 8.32 0.00 39.48 4.09
475 495 3.284617 ACGTGGGTAAGAGCTTGTTTTT 58.715 40.909 0.00 0.00 0.00 1.94
488 508 4.341235 AGCTTGTTTTTGGGGAGTTACTTC 59.659 41.667 0.00 0.00 0.00 3.01
530 550 1.002430 AGCTGCGATTTCACCTCTTGA 59.998 47.619 0.00 0.00 0.00 3.02
535 555 4.071423 TGCGATTTCACCTCTTGATTTGA 58.929 39.130 0.00 0.00 32.84 2.69
565 585 7.719778 TGATGCACATAGAGTTACATGAATC 57.280 36.000 0.00 0.00 0.00 2.52
590 610 1.286880 GGCTCTGTTGCAATGCGTT 59.713 52.632 0.59 0.00 34.04 4.84
591 611 0.730494 GGCTCTGTTGCAATGCGTTC 60.730 55.000 0.59 0.00 34.04 3.95
593 613 1.464608 GCTCTGTTGCAATGCGTTCTA 59.535 47.619 0.59 0.00 0.00 2.10
601 621 5.180304 TGTTGCAATGCGTTCTACTGAATAA 59.820 36.000 0.59 0.00 34.40 1.40
603 623 6.247727 TGCAATGCGTTCTACTGAATAAAA 57.752 33.333 0.00 0.00 34.40 1.52
689 716 8.682936 ATAAAGTTTGATGTATCTGCTTAGGG 57.317 34.615 0.00 0.00 0.00 3.53
690 717 5.957771 AGTTTGATGTATCTGCTTAGGGA 57.042 39.130 0.00 0.00 0.00 4.20
691 718 6.506538 AGTTTGATGTATCTGCTTAGGGAT 57.493 37.500 0.00 0.00 0.00 3.85
692 719 6.294473 AGTTTGATGTATCTGCTTAGGGATG 58.706 40.000 0.00 0.00 0.00 3.51
693 720 4.277515 TGATGTATCTGCTTAGGGATGC 57.722 45.455 0.00 0.00 0.00 3.91
694 721 3.647590 TGATGTATCTGCTTAGGGATGCA 59.352 43.478 0.00 0.00 38.49 3.96
695 722 4.102996 TGATGTATCTGCTTAGGGATGCAA 59.897 41.667 0.00 0.00 37.88 4.08
696 723 4.502105 TGTATCTGCTTAGGGATGCAAA 57.498 40.909 0.00 0.00 38.81 3.68
697 724 4.199310 TGTATCTGCTTAGGGATGCAAAC 58.801 43.478 0.00 0.00 38.81 2.93
698 725 2.877097 TCTGCTTAGGGATGCAAACA 57.123 45.000 0.00 0.00 38.81 2.83
699 726 2.715046 TCTGCTTAGGGATGCAAACAG 58.285 47.619 0.00 0.00 38.81 3.16
700 727 2.305635 TCTGCTTAGGGATGCAAACAGA 59.694 45.455 0.00 0.00 38.81 3.41
701 728 2.421424 CTGCTTAGGGATGCAAACAGAC 59.579 50.000 0.00 0.00 38.81 3.51
702 729 1.398390 GCTTAGGGATGCAAACAGACG 59.602 52.381 0.00 0.00 0.00 4.18
703 730 2.009774 CTTAGGGATGCAAACAGACGG 58.990 52.381 0.00 0.00 0.00 4.79
704 731 0.392461 TAGGGATGCAAACAGACGGC 60.392 55.000 0.00 0.00 0.00 5.68
705 732 2.480555 GGATGCAAACAGACGGCG 59.519 61.111 4.80 4.80 0.00 6.46
706 733 2.325082 GGATGCAAACAGACGGCGT 61.325 57.895 14.65 14.65 0.00 5.68
707 734 1.132640 GATGCAAACAGACGGCGTC 59.867 57.895 31.33 31.33 36.53 5.19
708 735 2.548587 GATGCAAACAGACGGCGTCG 62.549 60.000 31.59 26.87 37.67 5.12
709 736 4.072088 GCAAACAGACGGCGTCGG 62.072 66.667 32.83 32.83 41.39 4.79
710 737 2.660552 CAAACAGACGGCGTCGGT 60.661 61.111 34.13 34.13 42.18 4.69
711 738 2.660552 AAACAGACGGCGTCGGTG 60.661 61.111 38.28 30.38 39.77 4.94
712 739 3.141522 AAACAGACGGCGTCGGTGA 62.142 57.895 38.28 0.00 39.77 4.02
713 740 3.553437 AACAGACGGCGTCGGTGAG 62.553 63.158 38.28 25.42 39.77 3.51
723 750 4.287781 TCGGTGAGCGTTGGCGAA 62.288 61.111 3.30 0.00 46.35 4.70
724 751 3.342627 CGGTGAGCGTTGGCGAAA 61.343 61.111 0.00 0.00 46.35 3.46
725 752 2.556287 GGTGAGCGTTGGCGAAAG 59.444 61.111 0.00 0.00 46.35 2.62
763 790 9.639563 TTATCATGGTTATTAAAGCAATGAGGA 57.360 29.630 0.00 0.00 45.56 3.71
764 791 8.716674 ATCATGGTTATTAAAGCAATGAGGAT 57.283 30.769 0.00 0.00 45.56 3.24
765 792 8.537728 TCATGGTTATTAAAGCAATGAGGATT 57.462 30.769 0.00 0.00 45.56 3.01
766 793 9.639563 TCATGGTTATTAAAGCAATGAGGATTA 57.360 29.630 0.00 0.00 45.56 1.75
767 794 9.903682 CATGGTTATTAAAGCAATGAGGATTAG 57.096 33.333 0.00 0.00 45.56 1.73
768 795 9.646522 ATGGTTATTAAAGCAATGAGGATTAGT 57.353 29.630 0.00 0.00 45.56 2.24
777 804 9.643693 AAAGCAATGAGGATTAGTATGTTTTTG 57.356 29.630 0.00 0.00 0.00 2.44
778 805 7.775120 AGCAATGAGGATTAGTATGTTTTTGG 58.225 34.615 0.00 0.00 0.00 3.28
779 806 6.476706 GCAATGAGGATTAGTATGTTTTTGGC 59.523 38.462 0.00 0.00 0.00 4.52
780 807 7.631377 GCAATGAGGATTAGTATGTTTTTGGCT 60.631 37.037 0.00 0.00 0.00 4.75
781 808 7.961326 ATGAGGATTAGTATGTTTTTGGCTT 57.039 32.000 0.00 0.00 0.00 4.35
782 809 7.391148 TGAGGATTAGTATGTTTTTGGCTTC 57.609 36.000 0.00 0.00 0.00 3.86
783 810 6.093495 TGAGGATTAGTATGTTTTTGGCTTCG 59.907 38.462 0.00 0.00 0.00 3.79
784 811 5.944007 AGGATTAGTATGTTTTTGGCTTCGT 59.056 36.000 0.00 0.00 0.00 3.85
785 812 6.027749 GGATTAGTATGTTTTTGGCTTCGTG 58.972 40.000 0.00 0.00 0.00 4.35
786 813 3.915437 AGTATGTTTTTGGCTTCGTGG 57.085 42.857 0.00 0.00 0.00 4.94
787 814 3.482436 AGTATGTTTTTGGCTTCGTGGA 58.518 40.909 0.00 0.00 0.00 4.02
788 815 2.793278 ATGTTTTTGGCTTCGTGGAC 57.207 45.000 0.00 0.00 0.00 4.02
789 816 1.464734 TGTTTTTGGCTTCGTGGACA 58.535 45.000 0.00 0.00 0.00 4.02
790 817 1.819288 TGTTTTTGGCTTCGTGGACAA 59.181 42.857 0.00 0.00 31.67 3.18
791 818 2.159310 TGTTTTTGGCTTCGTGGACAAG 60.159 45.455 0.00 0.00 35.48 3.16
792 819 0.383949 TTTTGGCTTCGTGGACAAGC 59.616 50.000 0.00 0.00 44.79 4.01
793 820 1.781025 TTTGGCTTCGTGGACAAGCG 61.781 55.000 0.35 0.00 46.21 4.68
794 821 3.423154 GGCTTCGTGGACAAGCGG 61.423 66.667 0.35 0.00 46.21 5.52
795 822 2.357034 GCTTCGTGGACAAGCGGA 60.357 61.111 0.00 0.00 37.14 5.54
796 823 2.668280 GCTTCGTGGACAAGCGGAC 61.668 63.158 0.00 0.00 37.14 4.79
797 824 2.355363 TTCGTGGACAAGCGGACG 60.355 61.111 0.00 0.00 0.00 4.79
816 843 3.536917 CGTCCGCCTGCATCCCTA 61.537 66.667 0.00 0.00 0.00 3.53
817 844 2.872388 CGTCCGCCTGCATCCCTAT 61.872 63.158 0.00 0.00 0.00 2.57
818 845 1.532604 CGTCCGCCTGCATCCCTATA 61.533 60.000 0.00 0.00 0.00 1.31
819 846 0.905357 GTCCGCCTGCATCCCTATAT 59.095 55.000 0.00 0.00 0.00 0.86
820 847 1.134670 GTCCGCCTGCATCCCTATATC 60.135 57.143 0.00 0.00 0.00 1.63
821 848 1.198713 CCGCCTGCATCCCTATATCT 58.801 55.000 0.00 0.00 0.00 1.98
822 849 1.134580 CCGCCTGCATCCCTATATCTG 60.135 57.143 0.00 0.00 0.00 2.90
823 850 1.741732 CGCCTGCATCCCTATATCTGC 60.742 57.143 0.00 0.00 35.21 4.26
824 851 1.558756 GCCTGCATCCCTATATCTGCT 59.441 52.381 0.00 0.00 35.66 4.24
909 949 6.831976 ACTAGAAACACTTTGAAGGATCTGT 58.168 36.000 0.00 0.00 0.00 3.41
910 950 6.708054 ACTAGAAACACTTTGAAGGATCTGTG 59.292 38.462 0.00 0.00 0.00 3.66
924 964 7.716998 TGAAGGATCTGTGCCTTATTAATCTTC 59.283 37.037 0.00 0.00 45.43 2.87
928 968 6.662414 TCTGTGCCTTATTAATCTTCGTTG 57.338 37.500 0.00 0.00 0.00 4.10
1045 1086 3.385111 GTCGTACTCATCCCTCTCCAAAT 59.615 47.826 0.00 0.00 0.00 2.32
1070 1111 2.959484 GCTACCACAGCCAGGCAGA 61.959 63.158 15.80 0.00 45.23 4.26
1081 1122 1.427809 CCAGGCAGATCCTATGTCCA 58.572 55.000 0.00 0.00 45.52 4.02
1224 1266 6.769134 TCAACTATCAATCTGAAGACCGTA 57.231 37.500 0.00 0.00 0.00 4.02
1264 1308 3.669344 TTTCGCGCCCAAGCAAGG 61.669 61.111 0.00 0.00 39.83 3.61
1374 1420 2.426023 GTTCCGAGTGCACCACCT 59.574 61.111 14.63 0.00 34.49 4.00
1422 1468 0.745845 GTGCATACAGGGAGGTGCTG 60.746 60.000 0.00 0.00 38.37 4.41
1630 1680 0.721718 GTGTGATGCTTGCTACGACC 59.278 55.000 0.00 0.00 0.00 4.79
1671 1722 5.449177 GGCCTTATTGATCAACTACAACAGC 60.449 44.000 11.07 6.01 0.00 4.40
1747 1798 2.102252 TGGTTGAATTTGCCTGTTGGAC 59.898 45.455 0.00 0.00 34.57 4.02
1827 1878 8.581578 CAGGTATGTTTAATTTTGTACCCAACT 58.418 33.333 0.00 0.00 33.70 3.16
1840 1891 8.671384 TTTGTACCCAACTGATATATACTTGC 57.329 34.615 0.00 0.00 0.00 4.01
2018 2069 1.080093 TCTTGTAGTTGCTCGCCGG 60.080 57.895 0.00 0.00 0.00 6.13
2117 2168 7.821359 CAGTAAAATCTTCTCTCTGAATCCACA 59.179 37.037 0.00 0.00 33.71 4.17
2118 2169 8.547173 AGTAAAATCTTCTCTCTGAATCCACAT 58.453 33.333 0.00 0.00 33.71 3.21
2157 2208 8.853077 TTATCTGCTGGTGATATAATTCTTGG 57.147 34.615 0.00 0.00 0.00 3.61
2160 2211 5.376625 TGCTGGTGATATAATTCTTGGGAC 58.623 41.667 0.00 0.00 0.00 4.46
2203 2254 4.906065 TGCATGCTACTCATTTCATTCC 57.094 40.909 20.33 0.00 31.79 3.01
2270 2321 6.038603 GCATGTCCTGTTTGCTTATGAGATTA 59.961 38.462 0.00 0.00 33.61 1.75
2409 2460 5.819901 CCAGATTGGAGGAGAATTAACAGAC 59.180 44.000 0.00 0.00 40.96 3.51
2598 2649 6.648879 TGCAGCAAAGGTAATAAGAAAGTT 57.351 33.333 0.00 0.00 0.00 2.66
2600 2651 6.040391 TGCAGCAAAGGTAATAAGAAAGTTGT 59.960 34.615 0.00 0.00 0.00 3.32
2615 2666 8.908786 AAGAAAGTTGTGTCTGAGAATTATCA 57.091 30.769 2.26 2.26 0.00 2.15
2636 2687 4.039703 CACTGTTGTTTCAGATGTGCTTG 58.960 43.478 0.65 0.00 38.63 4.01
2683 2734 6.146021 GGTGGAAATCAGCACAATTTTAACAG 59.854 38.462 0.00 0.00 42.97 3.16
2686 2737 6.701400 GGAAATCAGCACAATTTTAACAGTGT 59.299 34.615 0.00 0.00 34.59 3.55
2733 4730 4.632153 AGTTTTTAGACATCGCACTGAGT 58.368 39.130 0.00 0.00 0.00 3.41
2764 4761 9.173021 TCTCTGAAGTTATTTGTCAAGTTTGAA 57.827 29.630 0.00 0.00 39.21 2.69
2776 4773 7.518731 TGTCAAGTTTGAAAGTGTTTATTGC 57.481 32.000 0.00 0.00 39.21 3.56
2787 4784 4.732784 AGTGTTTATTGCGGCATGTAAAG 58.267 39.130 16.49 0.00 0.00 1.85
2792 4789 7.911205 GTGTTTATTGCGGCATGTAAAGTAATA 59.089 33.333 16.49 2.33 0.00 0.98
2797 4794 6.503589 TGCGGCATGTAAAGTAATAGTTTT 57.496 33.333 0.00 0.00 0.00 2.43
2798 4795 6.318628 TGCGGCATGTAAAGTAATAGTTTTG 58.681 36.000 0.00 0.00 0.00 2.44
2802 4799 7.218204 CGGCATGTAAAGTAATAGTTTTGAAGC 59.782 37.037 0.00 0.22 0.00 3.86
2856 4854 9.601971 TTTTATTTTACGTAGAAACACATGCTC 57.398 29.630 2.33 0.00 0.00 4.26
2872 4870 3.815856 TGCTCTCTTCTCATTAGCCAG 57.184 47.619 0.00 0.00 32.14 4.85
2877 4875 4.614475 TCTCTTCTCATTAGCCAGAGGAA 58.386 43.478 0.00 0.00 33.64 3.36
2879 4877 4.357325 TCTTCTCATTAGCCAGAGGAAGT 58.643 43.478 0.00 0.00 32.76 3.01
2884 4882 5.958380 TCTCATTAGCCAGAGGAAGTCTTTA 59.042 40.000 0.00 0.00 30.64 1.85
2918 4916 3.806949 TGTCCTATGTTTGGCTTTCCT 57.193 42.857 0.00 0.00 0.00 3.36
2937 4935 7.175119 GCTTTCCTTGTTAAGAATCTTGTAGGT 59.825 37.037 5.64 0.00 0.00 3.08
2948 4946 5.645497 AGAATCTTGTAGGTTTCATCACAGC 59.355 40.000 0.00 0.00 0.00 4.40
2970 4968 7.289782 ACAGCTATCTCAGTATCCTTCTGATTT 59.710 37.037 0.00 0.00 40.46 2.17
2978 4976 7.624549 TCAGTATCCTTCTGATTTGTAGCTTT 58.375 34.615 0.00 0.00 37.07 3.51
2992 4990 8.748380 ATTTGTAGCTTTATCTCAAAACTTGC 57.252 30.769 0.00 0.00 32.99 4.01
3020 5018 1.884067 GCCTTTGTTGGGGTCTCTCTG 60.884 57.143 0.00 0.00 0.00 3.35
3199 5197 4.030913 TGCTAGTTCTAGCCATGGTAGTT 58.969 43.478 23.42 0.00 42.17 2.24
3298 5300 6.664428 AAATGTACAGCTTTTATTGGGTGT 57.336 33.333 0.33 0.00 44.59 4.16
3363 5365 3.746045 ATCAGTATGTTATCCGCCGTT 57.254 42.857 0.00 0.00 37.40 4.44
3368 5370 0.746563 ATGTTATCCGCCGTTGTGGG 60.747 55.000 0.00 0.00 42.73 4.61
3426 5428 3.570125 GCTCTTTTTAGCACTTGAAGGGT 59.430 43.478 0.00 0.00 42.30 4.34
3432 5434 6.969993 TTTTAGCACTTGAAGGGTGTAAAT 57.030 33.333 0.00 0.00 37.07 1.40
3602 5604 5.627172 TGCTATCGTCTAAAAATTGTGCAC 58.373 37.500 10.75 10.75 0.00 4.57
3608 5610 7.017498 TCGTCTAAAAATTGTGCACTTTGTA 57.983 32.000 19.41 9.53 0.00 2.41
3634 5636 3.950395 ACTGCTGGATTTCTGGCTTTATC 59.050 43.478 0.00 0.00 0.00 1.75
3641 5643 5.133322 TGGATTTCTGGCTTTATCATCCTCT 59.867 40.000 0.00 0.00 31.60 3.69
3651 5653 6.039829 GGCTTTATCATCCTCTCCGAATTTTT 59.960 38.462 0.00 0.00 0.00 1.94
3656 5658 6.546428 TCATCCTCTCCGAATTTTTAGACT 57.454 37.500 0.00 0.00 0.00 3.24
3664 5666 2.092323 GAATTTTTAGACTGGCCGCCT 58.908 47.619 11.61 0.00 0.00 5.52
3666 5668 0.109723 TTTTTAGACTGGCCGCCTGT 59.890 50.000 20.90 20.90 38.38 4.00
3698 5700 2.438434 CCCAACCATCGGGCTGTC 60.438 66.667 0.00 0.00 36.72 3.51
3734 5736 2.373707 GGGCAGACATGAGGAGGCT 61.374 63.158 0.00 0.00 0.00 4.58
3735 5737 1.050988 GGGCAGACATGAGGAGGCTA 61.051 60.000 0.00 0.00 0.00 3.93
3736 5738 0.105778 GGCAGACATGAGGAGGCTAC 59.894 60.000 0.00 0.00 0.00 3.58
3741 5744 1.589993 CATGAGGAGGCTACACGCG 60.590 63.158 3.53 3.53 40.44 6.01
3746 5749 3.542742 GAGGCTACACGCGTTCGC 61.543 66.667 10.22 12.59 40.44 4.70
3759 5762 0.526739 CGTTCGCCACATCGGATACA 60.527 55.000 0.00 0.00 36.56 2.29
3764 5767 1.829456 CCACATCGGATACAGCCCA 59.171 57.895 0.00 0.00 36.56 5.36
3765 5768 0.397941 CCACATCGGATACAGCCCAT 59.602 55.000 0.00 0.00 36.56 4.00
3766 5769 1.202806 CCACATCGGATACAGCCCATT 60.203 52.381 0.00 0.00 36.56 3.16
3767 5770 1.875514 CACATCGGATACAGCCCATTG 59.124 52.381 0.00 0.00 0.00 2.82
3769 5772 1.875514 CATCGGATACAGCCCATTGTG 59.124 52.381 0.00 0.00 32.56 3.33
3770 5773 0.180171 TCGGATACAGCCCATTGTGG 59.820 55.000 0.00 0.00 37.25 4.17
3799 5802 2.067386 GGCCCCATAAATACCCTACCA 58.933 52.381 0.00 0.00 0.00 3.25
3811 5814 1.004200 CCTACCAACGGCCGAAACT 60.004 57.895 35.90 13.74 0.00 2.66
3832 5835 6.031751 ACTCTAATCAAAGTCCACACTCTC 57.968 41.667 0.00 0.00 29.93 3.20
3837 5840 2.034685 TCAAAGTCCACACTCTCGACTG 59.965 50.000 0.00 0.00 36.97 3.51
3858 5861 1.474879 CTTCCACTCTTCGTCTCCTCC 59.525 57.143 0.00 0.00 0.00 4.30
3861 5864 0.323908 CACTCTTCGTCTCCTCCCCT 60.324 60.000 0.00 0.00 0.00 4.79
3862 5865 0.410270 ACTCTTCGTCTCCTCCCCTT 59.590 55.000 0.00 0.00 0.00 3.95
3863 5866 1.107945 CTCTTCGTCTCCTCCCCTTC 58.892 60.000 0.00 0.00 0.00 3.46
3864 5867 0.324460 TCTTCGTCTCCTCCCCTTCC 60.324 60.000 0.00 0.00 0.00 3.46
3865 5868 0.324830 CTTCGTCTCCTCCCCTTCCT 60.325 60.000 0.00 0.00 0.00 3.36
3866 5869 1.005228 TTCGTCTCCTCCCCTTCCTA 58.995 55.000 0.00 0.00 0.00 2.94
3872 5875 0.636932 TCCTCCCCTTCCTATCCCCT 60.637 60.000 0.00 0.00 0.00 4.79
3878 5881 1.735926 CCTTCCTATCCCCTTCCCTC 58.264 60.000 0.00 0.00 0.00 4.30
3887 5890 1.709994 CCCCTTCCCTCTACCATGGC 61.710 65.000 13.04 0.00 0.00 4.40
3889 5892 0.988145 CCTTCCCTCTACCATGGCCA 60.988 60.000 13.04 8.56 0.00 5.36
3894 5897 1.207791 CCTCTACCATGGCCAACTCT 58.792 55.000 10.96 0.00 0.00 3.24
3896 5899 1.833630 CTCTACCATGGCCAACTCTGA 59.166 52.381 10.96 5.18 0.00 3.27
3905 5908 1.606737 GGCCAACTCTGACAGTCACTC 60.607 57.143 0.00 0.00 32.30 3.51
3917 5920 1.072159 GTCACTCTGGCAGCACCTT 59.928 57.895 10.34 0.00 40.22 3.50
3921 5924 0.838122 ACTCTGGCAGCACCTTAGGT 60.838 55.000 10.34 0.00 40.22 3.08
3941 5944 3.132289 GGTAACGAGTCAGATCCCATTGA 59.868 47.826 0.00 0.00 0.00 2.57
3943 5946 1.482593 ACGAGTCAGATCCCATTGACC 59.517 52.381 8.72 1.87 43.64 4.02
3986 5989 2.669849 CTCCAGCAGCAAGGCTCT 59.330 61.111 0.00 0.00 43.68 4.09
3988 5991 2.750637 CCAGCAGCAAGGCTCTGG 60.751 66.667 16.58 16.58 43.68 3.86
3992 5995 1.077930 GCAGCAAGGCTCTGGATGA 60.078 57.895 5.48 0.00 36.40 2.92
3994 5997 1.088340 CAGCAAGGCTCTGGATGACG 61.088 60.000 0.00 0.00 36.40 4.35
3999 6002 1.039068 AGGCTCTGGATGACGATGAG 58.961 55.000 0.00 0.00 0.00 2.90
4030 6033 0.591170 CTTTGCCATCCAACGTTCGT 59.409 50.000 0.00 0.00 31.97 3.85
4073 6076 3.486252 CTTCGCCTCGTCCCCGATC 62.486 68.421 0.00 0.00 43.27 3.69
4100 6103 3.704908 ATGCAATTTGGCCGAGCGC 62.705 57.895 0.00 0.00 0.00 5.92
4134 6138 2.032376 TGCGCAACTGCAGATCCA 59.968 55.556 23.35 6.95 40.62 3.41
4138 6142 1.086067 CGCAACTGCAGATCCATCGT 61.086 55.000 23.35 0.00 42.21 3.73
4139 6143 1.089920 GCAACTGCAGATCCATCGTT 58.910 50.000 23.35 0.00 41.59 3.85
4164 6168 1.000771 GCCACTTCCCTTTCCCTCC 60.001 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 3.055021 GGGGAAGAAGTTGAAGGGAGTAG 60.055 52.174 0.00 0.00 0.00 2.57
14 15 2.910977 GGGGAAGAAGTTGAAGGGAGTA 59.089 50.000 0.00 0.00 0.00 2.59
18 19 1.076438 AGGGGGAAGAAGTTGAAGGG 58.924 55.000 0.00 0.00 0.00 3.95
36 37 2.089854 CGGCAAAGATGGACGGAAG 58.910 57.895 0.00 0.00 0.00 3.46
39 40 3.508840 GCCGGCAAAGATGGACGG 61.509 66.667 24.80 1.57 46.78 4.79
41 42 2.038269 TTCGCCGGCAAAGATGGAC 61.038 57.895 28.98 0.00 0.00 4.02
42 43 2.038269 GTTCGCCGGCAAAGATGGA 61.038 57.895 28.98 10.87 0.00 3.41
43 44 2.485122 GTTCGCCGGCAAAGATGG 59.515 61.111 28.98 8.23 0.00 3.51
44 45 2.098298 CGTTCGCCGGCAAAGATG 59.902 61.111 28.98 9.08 0.00 2.90
95 96 2.026301 GATCGTCGCGGGAGGAAG 59.974 66.667 25.50 8.16 40.17 3.46
96 97 3.884350 CGATCGTCGCGGGAGGAA 61.884 66.667 25.50 11.69 40.17 3.36
111 112 3.900892 GCGAGGATTCGGAGGCGA 61.901 66.667 0.00 0.00 46.76 5.54
148 158 2.732658 GCGGTACCGACCTATGGG 59.267 66.667 37.62 5.85 44.46 4.00
167 177 2.685380 AGGAGAACTGAGGGGGCG 60.685 66.667 0.00 0.00 0.00 6.13
177 188 2.182030 CGAGCCACGGAGGAGAAC 59.818 66.667 0.00 0.00 41.22 3.01
220 231 4.227134 CTCCATCCGTCCGCCCTG 62.227 72.222 0.00 0.00 0.00 4.45
264 275 0.320374 ATCAAACGACTCGGCAAGGA 59.680 50.000 2.98 0.00 0.00 3.36
285 296 5.868257 TGAATCAAACAATACTGCGTCATC 58.132 37.500 0.00 0.00 0.00 2.92
288 300 5.961843 CAGATGAATCAAACAATACTGCGTC 59.038 40.000 0.00 0.00 0.00 5.19
299 312 5.591099 ACAAACACCACAGATGAATCAAAC 58.409 37.500 0.00 0.00 0.00 2.93
381 399 6.371389 CAATTTCTGAAACCCTAGACGAAAC 58.629 40.000 4.73 0.00 0.00 2.78
411 429 0.515564 GCAAGCAAGCAAGCAATTGG 59.484 50.000 7.72 0.00 36.85 3.16
412 430 0.515564 GGCAAGCAAGCAAGCAATTG 59.484 50.000 0.00 0.00 36.85 2.32
413 431 0.604511 GGGCAAGCAAGCAAGCAATT 60.605 50.000 10.15 0.00 36.85 2.32
414 432 1.004200 GGGCAAGCAAGCAAGCAAT 60.004 52.632 10.15 0.00 36.85 3.56
421 441 2.740714 CGTCTACGGGCAAGCAAGC 61.741 63.158 0.00 0.00 35.37 4.01
422 442 2.740714 GCGTCTACGGGCAAGCAAG 61.741 63.158 4.49 0.00 40.23 4.01
429 449 1.736681 CTATACCTAGCGTCTACGGGC 59.263 57.143 4.49 0.00 40.23 6.13
435 455 5.174395 CACGTATACCTATACCTAGCGTCT 58.826 45.833 0.00 0.00 36.13 4.18
449 469 3.131755 ACAAGCTCTTACCCACGTATACC 59.868 47.826 0.00 0.00 0.00 2.73
452 472 3.975168 AACAAGCTCTTACCCACGTAT 57.025 42.857 0.00 0.00 0.00 3.06
453 473 3.756933 AAACAAGCTCTTACCCACGTA 57.243 42.857 0.00 0.00 0.00 3.57
454 474 2.632987 AAACAAGCTCTTACCCACGT 57.367 45.000 0.00 0.00 0.00 4.49
455 475 3.550030 CCAAAAACAAGCTCTTACCCACG 60.550 47.826 0.00 0.00 0.00 4.94
459 479 3.227614 TCCCCAAAAACAAGCTCTTACC 58.772 45.455 0.00 0.00 0.00 2.85
461 481 4.178956 ACTCCCCAAAAACAAGCTCTTA 57.821 40.909 0.00 0.00 0.00 2.10
462 482 3.032265 ACTCCCCAAAAACAAGCTCTT 57.968 42.857 0.00 0.00 0.00 2.85
463 483 2.755952 ACTCCCCAAAAACAAGCTCT 57.244 45.000 0.00 0.00 0.00 4.09
465 485 3.910989 AGTAACTCCCCAAAAACAAGCT 58.089 40.909 0.00 0.00 0.00 3.74
467 487 4.261447 CCGAAGTAACTCCCCAAAAACAAG 60.261 45.833 0.00 0.00 0.00 3.16
475 495 0.472352 ACACCCGAAGTAACTCCCCA 60.472 55.000 0.00 0.00 0.00 4.96
488 508 1.002900 CACTACAGCAAAACACACCCG 60.003 52.381 0.00 0.00 0.00 5.28
530 550 6.827251 ACTCTATGTGCATCATGAGTTCAAAT 59.173 34.615 17.67 2.40 39.46 2.32
535 555 6.643388 TGTAACTCTATGTGCATCATGAGTT 58.357 36.000 26.09 26.09 45.29 3.01
565 585 1.771073 TTGCAACAGAGCCACGAACG 61.771 55.000 0.00 0.00 0.00 3.95
593 613 9.525409 GCATTCTAATTGAGCATTTTATTCAGT 57.475 29.630 0.00 0.00 0.00 3.41
601 621 7.870509 TGAGTAGCATTCTAATTGAGCATTT 57.129 32.000 0.00 0.00 0.00 2.32
603 623 7.555554 ACTTTGAGTAGCATTCTAATTGAGCAT 59.444 33.333 0.00 0.00 0.00 3.79
676 703 4.199310 TGTTTGCATCCCTAAGCAGATAC 58.801 43.478 0.00 0.00 42.39 2.24
685 712 0.392461 GCCGTCTGTTTGCATCCCTA 60.392 55.000 0.00 0.00 0.00 3.53
686 713 1.675641 GCCGTCTGTTTGCATCCCT 60.676 57.895 0.00 0.00 0.00 4.20
687 714 2.877691 GCCGTCTGTTTGCATCCC 59.122 61.111 0.00 0.00 0.00 3.85
688 715 2.240612 GACGCCGTCTGTTTGCATCC 62.241 60.000 10.56 0.00 0.00 3.51
689 716 1.132640 GACGCCGTCTGTTTGCATC 59.867 57.895 10.56 0.00 0.00 3.91
690 717 2.667318 CGACGCCGTCTGTTTGCAT 61.667 57.895 16.07 0.00 0.00 3.96
691 718 3.334751 CGACGCCGTCTGTTTGCA 61.335 61.111 16.07 0.00 0.00 4.08
692 719 4.072088 CCGACGCCGTCTGTTTGC 62.072 66.667 16.07 0.00 0.00 3.68
693 720 2.660552 ACCGACGCCGTCTGTTTG 60.661 61.111 16.07 0.00 0.00 2.93
694 721 2.660552 CACCGACGCCGTCTGTTT 60.661 61.111 16.07 0.00 28.05 2.83
695 722 3.553437 CTCACCGACGCCGTCTGTT 62.553 63.158 16.07 0.00 28.05 3.16
696 723 4.039357 CTCACCGACGCCGTCTGT 62.039 66.667 16.07 12.31 30.53 3.41
706 733 3.793775 TTTCGCCAACGCTCACCGA 62.794 57.895 0.00 0.00 41.02 4.69
707 734 3.295228 CTTTCGCCAACGCTCACCG 62.295 63.158 0.00 0.00 44.21 4.94
708 735 2.556287 CTTTCGCCAACGCTCACC 59.444 61.111 0.00 0.00 39.84 4.02
709 736 2.127232 GCTTTCGCCAACGCTCAC 60.127 61.111 0.00 0.00 39.84 3.51
710 737 0.672091 TATGCTTTCGCCAACGCTCA 60.672 50.000 0.00 0.00 39.84 4.26
711 738 0.446222 TTATGCTTTCGCCAACGCTC 59.554 50.000 0.00 0.00 39.84 5.03
712 739 1.094785 ATTATGCTTTCGCCAACGCT 58.905 45.000 0.00 0.00 39.84 5.07
713 740 1.908065 AATTATGCTTTCGCCAACGC 58.092 45.000 0.00 0.00 39.84 4.84
714 741 4.530094 TCTAATTATGCTTTCGCCAACG 57.470 40.909 0.00 0.00 42.01 4.10
715 742 9.118236 GATAATTCTAATTATGCTTTCGCCAAC 57.882 33.333 11.67 0.00 40.63 3.77
716 743 8.845227 TGATAATTCTAATTATGCTTTCGCCAA 58.155 29.630 11.67 0.00 40.63 4.52
717 744 8.389779 TGATAATTCTAATTATGCTTTCGCCA 57.610 30.769 11.67 0.68 40.63 5.69
718 745 9.282247 CATGATAATTCTAATTATGCTTTCGCC 57.718 33.333 11.67 0.00 40.63 5.54
719 746 9.282247 CCATGATAATTCTAATTATGCTTTCGC 57.718 33.333 11.67 0.00 40.63 4.70
737 764 9.639563 TCCTCATTGCTTTAATAACCATGATAA 57.360 29.630 0.00 0.00 0.00 1.75
738 765 9.812347 ATCCTCATTGCTTTAATAACCATGATA 57.188 29.630 0.00 0.00 0.00 2.15
739 766 8.716674 ATCCTCATTGCTTTAATAACCATGAT 57.283 30.769 0.00 0.00 0.00 2.45
740 767 8.537728 AATCCTCATTGCTTTAATAACCATGA 57.462 30.769 0.00 0.00 0.00 3.07
741 768 9.903682 CTAATCCTCATTGCTTTAATAACCATG 57.096 33.333 0.00 0.00 0.00 3.66
742 769 9.646522 ACTAATCCTCATTGCTTTAATAACCAT 57.353 29.630 0.00 0.00 0.00 3.55
751 778 9.643693 CAAAAACATACTAATCCTCATTGCTTT 57.356 29.630 0.00 0.00 0.00 3.51
752 779 8.253113 CCAAAAACATACTAATCCTCATTGCTT 58.747 33.333 0.00 0.00 0.00 3.91
753 780 7.631377 GCCAAAAACATACTAATCCTCATTGCT 60.631 37.037 0.00 0.00 0.00 3.91
754 781 6.476706 GCCAAAAACATACTAATCCTCATTGC 59.523 38.462 0.00 0.00 0.00 3.56
755 782 7.775120 AGCCAAAAACATACTAATCCTCATTG 58.225 34.615 0.00 0.00 0.00 2.82
756 783 7.961326 AGCCAAAAACATACTAATCCTCATT 57.039 32.000 0.00 0.00 0.00 2.57
757 784 7.201732 CGAAGCCAAAAACATACTAATCCTCAT 60.202 37.037 0.00 0.00 0.00 2.90
758 785 6.093495 CGAAGCCAAAAACATACTAATCCTCA 59.907 38.462 0.00 0.00 0.00 3.86
759 786 6.093633 ACGAAGCCAAAAACATACTAATCCTC 59.906 38.462 0.00 0.00 0.00 3.71
760 787 5.944007 ACGAAGCCAAAAACATACTAATCCT 59.056 36.000 0.00 0.00 0.00 3.24
761 788 6.027749 CACGAAGCCAAAAACATACTAATCC 58.972 40.000 0.00 0.00 0.00 3.01
762 789 6.027749 CCACGAAGCCAAAAACATACTAATC 58.972 40.000 0.00 0.00 0.00 1.75
763 790 5.708230 TCCACGAAGCCAAAAACATACTAAT 59.292 36.000 0.00 0.00 0.00 1.73
764 791 5.049267 GTCCACGAAGCCAAAAACATACTAA 60.049 40.000 0.00 0.00 0.00 2.24
765 792 4.453136 GTCCACGAAGCCAAAAACATACTA 59.547 41.667 0.00 0.00 0.00 1.82
766 793 3.252458 GTCCACGAAGCCAAAAACATACT 59.748 43.478 0.00 0.00 0.00 2.12
767 794 3.003897 TGTCCACGAAGCCAAAAACATAC 59.996 43.478 0.00 0.00 0.00 2.39
768 795 3.215151 TGTCCACGAAGCCAAAAACATA 58.785 40.909 0.00 0.00 0.00 2.29
769 796 2.028130 TGTCCACGAAGCCAAAAACAT 58.972 42.857 0.00 0.00 0.00 2.71
770 797 1.464734 TGTCCACGAAGCCAAAAACA 58.535 45.000 0.00 0.00 0.00 2.83
771 798 2.459934 CTTGTCCACGAAGCCAAAAAC 58.540 47.619 0.00 0.00 0.00 2.43
772 799 1.202359 GCTTGTCCACGAAGCCAAAAA 60.202 47.619 0.00 0.00 40.03 1.94
773 800 0.383949 GCTTGTCCACGAAGCCAAAA 59.616 50.000 0.00 0.00 40.03 2.44
774 801 1.781025 CGCTTGTCCACGAAGCCAAA 61.781 55.000 0.00 0.00 42.45 3.28
775 802 2.250939 CGCTTGTCCACGAAGCCAA 61.251 57.895 0.00 0.00 42.45 4.52
776 803 2.664851 CGCTTGTCCACGAAGCCA 60.665 61.111 0.00 0.00 42.45 4.75
777 804 3.423154 CCGCTTGTCCACGAAGCC 61.423 66.667 0.00 0.00 42.45 4.35
778 805 2.357034 TCCGCTTGTCCACGAAGC 60.357 61.111 0.00 0.00 42.08 3.86
779 806 2.372690 CGTCCGCTTGTCCACGAAG 61.373 63.158 0.00 0.00 34.06 3.79
780 807 2.355363 CGTCCGCTTGTCCACGAA 60.355 61.111 0.00 0.00 34.06 3.85
799 826 1.532604 TATAGGGATGCAGGCGGACG 61.533 60.000 0.00 0.00 0.00 4.79
800 827 0.905357 ATATAGGGATGCAGGCGGAC 59.095 55.000 0.00 0.00 0.00 4.79
801 828 1.195115 GATATAGGGATGCAGGCGGA 58.805 55.000 0.00 0.00 0.00 5.54
802 829 1.134580 CAGATATAGGGATGCAGGCGG 60.135 57.143 0.00 0.00 0.00 6.13
803 830 1.741732 GCAGATATAGGGATGCAGGCG 60.742 57.143 0.00 0.00 38.54 5.52
804 831 1.558756 AGCAGATATAGGGATGCAGGC 59.441 52.381 0.00 0.00 41.14 4.85
805 832 4.029520 ACTAGCAGATATAGGGATGCAGG 58.970 47.826 0.00 0.00 41.14 4.85
806 833 6.039270 GTCTACTAGCAGATATAGGGATGCAG 59.961 46.154 0.00 0.00 41.14 4.41
807 834 5.888724 GTCTACTAGCAGATATAGGGATGCA 59.111 44.000 0.00 0.00 41.14 3.96
808 835 5.888724 TGTCTACTAGCAGATATAGGGATGC 59.111 44.000 0.00 0.00 38.97 3.91
809 836 7.946381 TTGTCTACTAGCAGATATAGGGATG 57.054 40.000 0.00 0.00 0.00 3.51
849 876 2.519013 ACAAGCTCATTCTTTCACCCC 58.481 47.619 0.00 0.00 0.00 4.95
882 909 5.623956 TCCTTCAAAGTGTTTCTAGTCCA 57.376 39.130 0.00 0.00 0.00 4.02
891 931 2.887152 GGCACAGATCCTTCAAAGTGTT 59.113 45.455 0.00 0.00 0.00 3.32
909 949 4.265893 TGGCAACGAAGATTAATAAGGCA 58.734 39.130 0.00 0.00 42.51 4.75
910 950 4.893424 TGGCAACGAAGATTAATAAGGC 57.107 40.909 0.00 0.00 42.51 4.35
952 993 7.826744 TCATGTAGGTAATAAGCAATGACACAA 59.173 33.333 0.00 0.00 0.00 3.33
1007 1048 1.069513 ACGACGTCACTTCATTTGGGA 59.930 47.619 17.16 0.00 0.00 4.37
1070 1111 4.756564 TGGAGCTAGATTGGACATAGGAT 58.243 43.478 0.00 0.00 0.00 3.24
1081 1122 4.851639 ATGTGTTTCCTGGAGCTAGATT 57.148 40.909 0.00 0.00 0.00 2.40
1224 1266 1.185618 TCGCAGCAAGACCACCTAGT 61.186 55.000 0.00 0.00 0.00 2.57
1264 1308 0.664761 CGTGATGCATCATCCCCAAC 59.335 55.000 30.89 15.66 39.87 3.77
1422 1468 2.004408 ATTCTGGGGGATCTGCCTGC 62.004 60.000 0.00 0.00 36.66 4.85
1630 1680 0.460987 GCCTGGAGTGGATCAAGTCG 60.461 60.000 0.00 0.00 0.00 4.18
1671 1722 2.202878 GCAGGCTGCATGGCATTG 60.203 61.111 33.33 0.00 44.26 2.82
1827 1878 7.038799 TGAGCTCTGGAATGCAAGTATATATCA 60.039 37.037 16.19 0.00 0.00 2.15
1840 1891 1.288350 CGCTTCTGAGCTCTGGAATG 58.712 55.000 19.23 14.20 46.96 2.67
1865 1916 9.802039 AATCTAGAAACCTACACATACCAAAAA 57.198 29.630 0.00 0.00 0.00 1.94
1937 1988 2.282040 GTGAGCACAGCAAGCCCT 60.282 61.111 0.00 0.00 0.00 5.19
2018 2069 2.492012 GCAGACCATGATCCATCTGAC 58.508 52.381 13.74 4.92 40.92 3.51
2117 2168 2.874701 CAGATAAGCTTAGGCGTTGCAT 59.125 45.455 12.54 0.00 44.37 3.96
2118 2169 2.279741 CAGATAAGCTTAGGCGTTGCA 58.720 47.619 12.54 0.00 44.37 4.08
2176 2227 4.945543 TGAAATGAGTAGCATGCATGTTCT 59.054 37.500 26.79 20.66 37.28 3.01
2188 2239 7.767659 TGAAGATCACAGGAATGAAATGAGTAG 59.232 37.037 0.00 0.00 30.82 2.57
2245 2296 3.691118 TCTCATAAGCAAACAGGACATGC 59.309 43.478 0.00 0.00 40.34 4.06
2270 2321 8.209584 ACATAAACTTGTCTCTGATATCATGCT 58.790 33.333 5.72 0.00 0.00 3.79
2421 2472 6.373774 CCTTGACAGCTTTAAGATCATGAAGT 59.626 38.462 0.00 0.00 0.00 3.01
2598 2649 6.524734 ACAACAGTGATAATTCTCAGACACA 58.475 36.000 0.00 0.00 0.00 3.72
2600 2651 7.714813 TGAAACAACAGTGATAATTCTCAGACA 59.285 33.333 0.00 0.00 0.00 3.41
2614 2665 3.976793 AGCACATCTGAAACAACAGTG 57.023 42.857 0.00 0.00 38.79 3.66
2615 2666 3.947196 TCAAGCACATCTGAAACAACAGT 59.053 39.130 0.00 0.00 38.79 3.55
2636 2687 8.571336 CCACCCATTTCAGTCATTTCTAATATC 58.429 37.037 0.00 0.00 0.00 1.63
2719 4716 1.127582 GAGCAAACTCAGTGCGATGTC 59.872 52.381 0.00 0.00 46.86 3.06
2722 4719 1.274728 AGAGAGCAAACTCAGTGCGAT 59.725 47.619 0.00 0.00 46.86 4.58
2726 4723 3.726607 ACTTCAGAGAGCAAACTCAGTG 58.273 45.455 0.00 0.00 46.09 3.66
2733 4730 7.283127 ACTTGACAAATAACTTCAGAGAGCAAA 59.717 33.333 0.00 0.00 0.00 3.68
2764 4761 4.775058 TTACATGCCGCAATAAACACTT 57.225 36.364 0.00 0.00 0.00 3.16
2776 4773 7.218204 GCTTCAAAACTATTACTTTACATGCCG 59.782 37.037 0.00 0.00 0.00 5.69
2829 4826 9.953697 AGCATGTGTTTCTACGTAAAATAAAAA 57.046 25.926 0.00 0.00 0.00 1.94
2830 4827 9.601971 GAGCATGTGTTTCTACGTAAAATAAAA 57.398 29.630 0.00 0.00 0.00 1.52
2831 4828 8.995220 AGAGCATGTGTTTCTACGTAAAATAAA 58.005 29.630 0.00 0.00 0.00 1.40
2832 4829 8.542497 AGAGCATGTGTTTCTACGTAAAATAA 57.458 30.769 0.00 0.00 0.00 1.40
2833 4830 8.033038 AGAGAGCATGTGTTTCTACGTAAAATA 58.967 33.333 0.00 0.00 0.00 1.40
2835 4832 6.220930 AGAGAGCATGTGTTTCTACGTAAAA 58.779 36.000 0.00 0.00 0.00 1.52
2836 4833 5.779922 AGAGAGCATGTGTTTCTACGTAAA 58.220 37.500 0.00 0.00 0.00 2.01
2837 4834 5.386958 AGAGAGCATGTGTTTCTACGTAA 57.613 39.130 0.00 0.00 0.00 3.18
2838 4835 5.183331 AGAAGAGAGCATGTGTTTCTACGTA 59.817 40.000 0.00 0.00 0.00 3.57
2839 4836 3.944055 AGAGAGCATGTGTTTCTACGT 57.056 42.857 0.00 0.00 0.00 3.57
2840 4837 4.489810 AGAAGAGAGCATGTGTTTCTACG 58.510 43.478 0.00 0.00 0.00 3.51
2841 4838 5.473931 TGAGAAGAGAGCATGTGTTTCTAC 58.526 41.667 0.00 0.00 0.00 2.59
2845 4843 5.353678 GCTAATGAGAAGAGAGCATGTGTTT 59.646 40.000 0.00 0.00 33.26 2.83
2846 4844 4.874966 GCTAATGAGAAGAGAGCATGTGTT 59.125 41.667 0.00 0.00 33.26 3.32
2853 4851 3.243839 CCTCTGGCTAATGAGAAGAGAGC 60.244 52.174 10.50 0.00 37.28 4.09
2856 4854 4.405358 ACTTCCTCTGGCTAATGAGAAGAG 59.595 45.833 0.00 4.02 35.94 2.85
2897 4895 4.322057 AGGAAAGCCAAACATAGGACAT 57.678 40.909 0.00 0.00 36.29 3.06
2899 4897 3.826729 ACAAGGAAAGCCAAACATAGGAC 59.173 43.478 0.00 0.00 36.29 3.85
2903 4901 7.589958 TTCTTAACAAGGAAAGCCAAACATA 57.410 32.000 0.00 0.00 36.29 2.29
2918 4916 9.567776 TGATGAAACCTACAAGATTCTTAACAA 57.432 29.630 0.00 0.00 0.00 2.83
2937 4935 6.753180 GGATACTGAGATAGCTGTGATGAAA 58.247 40.000 0.00 0.00 0.00 2.69
2970 4968 6.875948 TGCAAGTTTTGAGATAAAGCTACA 57.124 33.333 0.00 0.00 0.00 2.74
2978 4976 5.437289 CACCTGTTGCAAGTTTTGAGATA 57.563 39.130 0.00 0.00 0.00 1.98
2992 4990 0.104671 CCCAACAAAGGCACCTGTTG 59.895 55.000 15.40 15.40 46.11 3.33
3020 5018 2.225727 GGTTGTCACGACATTTCCTTCC 59.774 50.000 0.00 0.00 41.52 3.46
3130 5128 0.036875 AGCTGAGTACAAGGGTTGCC 59.963 55.000 0.00 0.00 0.00 4.52
3146 5144 6.788598 TTTGAGAACAGATCATCTAGAGCT 57.211 37.500 0.00 0.00 45.65 4.09
3199 5197 3.483808 TGTACACCACTGAATGCTGAA 57.516 42.857 0.00 0.00 0.00 3.02
3225 5227 8.371699 GGACTGTTCCTAGCATATTTTAGAGAT 58.628 37.037 0.00 0.00 39.13 2.75
3226 5228 7.727181 GGACTGTTCCTAGCATATTTTAGAGA 58.273 38.462 0.00 0.00 39.13 3.10
3227 5229 7.954788 GGACTGTTCCTAGCATATTTTAGAG 57.045 40.000 0.00 0.00 39.13 2.43
3298 5300 3.138304 GGACACATACTTGCAGTGAACA 58.862 45.455 9.75 0.00 37.05 3.18
3363 5365 3.255395 CACACTGCAATAATCAACCCACA 59.745 43.478 0.00 0.00 0.00 4.17
3368 5370 4.796830 CAGCATCACACTGCAATAATCAAC 59.203 41.667 0.00 0.00 44.77 3.18
3426 5428 7.385267 ACAAGCCAAATCAAGCAATATTTACA 58.615 30.769 0.00 0.00 0.00 2.41
3592 5594 7.169645 CAGCAGTATTTACAAAGTGCACAATTT 59.830 33.333 21.04 9.01 33.24 1.82
3602 5604 7.253422 CCAGAAATCCAGCAGTATTTACAAAG 58.747 38.462 0.00 0.00 0.00 2.77
3608 5610 3.973425 AGCCAGAAATCCAGCAGTATTT 58.027 40.909 0.00 0.00 0.00 1.40
3634 5636 5.525378 CCAGTCTAAAAATTCGGAGAGGATG 59.475 44.000 0.00 0.00 38.43 3.51
3641 5643 2.352388 CGGCCAGTCTAAAAATTCGGA 58.648 47.619 2.24 0.00 0.00 4.55
3651 5653 1.756950 CCTACAGGCGGCCAGTCTA 60.757 63.158 21.00 3.50 30.67 2.59
3656 5658 2.606519 AGTTCCTACAGGCGGCCA 60.607 61.111 23.09 0.00 34.44 5.36
3696 5698 1.475751 CCAGATATGTGGGTGCCAGAC 60.476 57.143 11.13 0.00 32.34 3.51
3698 5700 3.409201 CCAGATATGTGGGTGCCAG 57.591 57.895 11.13 0.00 32.34 4.85
3734 5736 2.048970 ATGTGGCGAACGCGTGTA 60.049 55.556 14.98 0.00 43.06 2.90
3735 5737 3.411351 GATGTGGCGAACGCGTGT 61.411 61.111 14.98 2.40 43.06 4.49
3736 5738 4.483683 CGATGTGGCGAACGCGTG 62.484 66.667 14.98 1.19 43.06 5.34
3741 5744 1.209128 CTGTATCCGATGTGGCGAAC 58.791 55.000 0.00 0.00 37.80 3.95
3746 5749 0.397941 ATGGGCTGTATCCGATGTGG 59.602 55.000 0.00 0.00 40.09 4.17
3771 5774 0.105038 ATTTATGGGGCCATGGTGGG 60.105 55.000 14.67 0.00 38.19 4.61
3772 5775 2.247358 GTATTTATGGGGCCATGGTGG 58.753 52.381 14.67 0.00 41.55 4.61
3773 5776 2.247358 GGTATTTATGGGGCCATGGTG 58.753 52.381 14.67 0.00 37.82 4.17
3774 5777 1.149077 GGGTATTTATGGGGCCATGGT 59.851 52.381 14.67 0.00 37.82 3.55
3775 5778 1.432807 AGGGTATTTATGGGGCCATGG 59.567 52.381 7.63 7.63 37.82 3.66
3776 5779 2.999185 AGGGTATTTATGGGGCCATG 57.001 50.000 4.39 0.00 37.82 3.66
3777 5780 2.652857 GGTAGGGTATTTATGGGGCCAT 59.347 50.000 4.39 0.00 40.19 4.40
3799 5802 2.754946 TGATTAGAGTTTCGGCCGTT 57.245 45.000 27.15 9.57 0.00 4.44
3811 5814 4.765339 TCGAGAGTGTGGACTTTGATTAGA 59.235 41.667 0.00 0.00 30.16 2.10
3832 5835 0.039074 ACGAAGAGTGGAAGCAGTCG 60.039 55.000 0.00 0.00 0.00 4.18
3837 5840 0.892063 AGGAGACGAAGAGTGGAAGC 59.108 55.000 0.00 0.00 0.00 3.86
3858 5861 0.272235 AGGGAAGGGGATAGGAAGGG 59.728 60.000 0.00 0.00 0.00 3.95
3861 5864 2.181642 GGTAGAGGGAAGGGGATAGGAA 59.818 54.545 0.00 0.00 0.00 3.36
3862 5865 1.793902 GGTAGAGGGAAGGGGATAGGA 59.206 57.143 0.00 0.00 0.00 2.94
3863 5866 1.508185 TGGTAGAGGGAAGGGGATAGG 59.492 57.143 0.00 0.00 0.00 2.57
3864 5867 3.177228 CATGGTAGAGGGAAGGGGATAG 58.823 54.545 0.00 0.00 0.00 2.08
3865 5868 2.158004 CCATGGTAGAGGGAAGGGGATA 60.158 54.545 2.57 0.00 0.00 2.59
3866 5869 1.416608 CCATGGTAGAGGGAAGGGGAT 60.417 57.143 2.57 0.00 0.00 3.85
3872 5875 0.623723 GTTGGCCATGGTAGAGGGAA 59.376 55.000 14.67 0.00 0.00 3.97
3878 5881 1.278985 TGTCAGAGTTGGCCATGGTAG 59.721 52.381 14.67 0.00 0.00 3.18
3887 5890 2.288702 CCAGAGTGACTGTCAGAGTTGG 60.289 54.545 11.41 12.39 44.40 3.77
3889 5892 1.342819 GCCAGAGTGACTGTCAGAGTT 59.657 52.381 11.41 0.00 44.40 3.01
3894 5897 1.368950 GCTGCCAGAGTGACTGTCA 59.631 57.895 6.36 6.36 44.40 3.58
3896 5899 1.070445 GTGCTGCCAGAGTGACTGT 59.930 57.895 0.00 0.00 44.40 3.55
3905 5908 1.739067 GTTACCTAAGGTGCTGCCAG 58.261 55.000 0.00 0.00 40.61 4.85
3907 5910 0.248289 TCGTTACCTAAGGTGCTGCC 59.752 55.000 0.00 0.00 36.19 4.85
3917 5920 3.657398 TGGGATCTGACTCGTTACCTA 57.343 47.619 0.00 0.00 0.00 3.08
3921 5924 3.132289 GGTCAATGGGATCTGACTCGTTA 59.868 47.826 11.35 0.00 41.43 3.18
3941 5944 0.610687 CTTCAAGAGCTCTTCCCGGT 59.389 55.000 26.18 1.11 33.11 5.28
3943 5946 0.898320 TCCTTCAAGAGCTCTTCCCG 59.102 55.000 26.18 15.31 33.11 5.14
3979 5982 1.411977 CTCATCGTCATCCAGAGCCTT 59.588 52.381 0.00 0.00 0.00 4.35
3985 5988 1.931841 CACAAGCTCATCGTCATCCAG 59.068 52.381 0.00 0.00 0.00 3.86
3986 5989 2.008543 GCACAAGCTCATCGTCATCCA 61.009 52.381 0.00 0.00 37.91 3.41
3999 6002 1.372623 GGCAAAGCAGAGCACAAGC 60.373 57.895 0.00 0.00 42.56 4.01
4030 6033 2.141011 CTCCTGCCAATGTCCACCCA 62.141 60.000 0.00 0.00 0.00 4.51
4073 6076 0.390124 CCAAATTGCATCATCGGGGG 59.610 55.000 0.00 0.00 0.00 5.40
4074 6077 0.249573 GCCAAATTGCATCATCGGGG 60.250 55.000 0.00 0.00 0.00 5.73
4080 6083 1.512230 GCTCGGCCAAATTGCATCA 59.488 52.632 2.24 0.00 0.00 3.07
4139 6143 2.384933 AAAGGGAAGTGGCATGCCCA 62.385 55.000 33.44 18.73 43.20 5.36


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.